I do tricep isolation exercises all the time, but don't really get pain in my elbows. I go pretty heavy too. It could be you're not doing the exercise properly, or (like Lucifuge said) you're going too heavy. Put some liniment on your elbows before you lift on days that you're going to do triceps and see if it helps.
If you still want to do them, you can search for alternatives that stress your elbows less. Standing overhead triceps extensions are better than seated ones, for example. Clever use of cables can also spare your elbows a lot.
My buddy has the same issue. I used to feel it somewhat in my elbows but not anymore. I don't do to much direct arm work though.
"A child does not learn to squat from the top down -- in other words, he does not suddenly make a conscious decision one day to squat. Actually, he is squatting one day and makes the conscious decision to stand." - Gray Cook